Talk:Creationism2

I am going to create a comprehensive wiki article on Creationism and Evolution here as part of a series of political articles I'm writing for my wiki at Bereawiki.com. I figured I would share this article with Creationwiki though since it's the main topic here. Enjoy!

Also, this is just a holding place for the material, feel free to merge it into the main Creationism article or anywhere else that it would be useful and delete this page afterward. I am writing the article from scratch and just needed a place for it. --Jzyehoshua 01:00, 13 July 2014 (EDT)

I am still working on the page, I think it might take another day or two to finish. I'll let everyone know when it is done. I am thinking of writing a section in the page on flaws in evolution as well, but either way there's still more material I want to include to make this page a truly definitive discussion of the subject. --Jzyehoshua 01:21, 14 July 2014 (EDT)

Finished!

Alright, I guess I am finished here. Feel free to merge this material into the main Creationism article or wherever else it would be useful. It still needs some internal link changes, probably some images, but should be otherwise ready. I didn't create it in the main Creationism article because A) I wanted to be able to easily copy my work over to my wiki, and B) given the size of what I'd be writing I didn't want to mess with the normal page structure. This way you can decide what to move to the main article. Best of luck with Creationwiki! I will probably check back later, I come and go. :)

-Joshua

Good stuff... Will definitely read it soon. Hope to see more contributions in the future.--Tsommer 00:21, 20 July 2014 (EDT)

Endogenous retroviruses

"Evolutionists" do not claim that retroviruses integrate their genomes in entirely random locations. There are statistical tendencies to integrate in certain types of locations, but this does not rescue special creation. For that, you would need integration to occur, unfailingly, every time at one specific (down to the base-pair) location. Surveys of actual integration sites prove that this does not happen. http://tinyurl.com/myheqhp

It is known that some retroviruses can infect different species independently. The article omits to say that endogenous integrations from these retroviruses are invariably to different loci in the different species. It is how we know that an ERV found in distantly related species is not there in both species by inheritance from a common ancestor. Creationists have to omit this information, because it destroys their "case". http://tinyurl.com/mmy9mvf

ERVs are perfectly well understood. http://tinyurl.com/nyod4ur

Re. a cure for AIDS, what better way to get "evolutionists" to sit up and take notice of the creo/IDists, but to find a cure themselves? If all the creationist/ID "research institutes" pooled their resources, I expect they could come up with a cure by next Thursday. About teatime. Barry Desborough 11:50, 21 November 2014 (EST)

When I've talked with evolutionists the argument on ERVs I've seen presented is based on the assumption integration is completely random. The only way to argue ERVs are proof for evolution is if they contain remnants that originated entirely through random processes. That way the evolutionist can say "see, these only can occur randomly, and thus for different species to have them shows a common ancestor." If the same sequences could arise independently in different species through a common cause, then there is no longer a reason to assume a common ancestor. Nor am I the only one who has experienced evolutionists using this argument that the sequences are random:

http://www.reasons.org/articles/does-retroviral-dna-insert-randomly-into-genomes

This argument actually has been made in one form or another, for example relating to transposons, since the 1970s by TalkOrigins:

"As explained above, observed gene duplications are rare and random events. Thus, it is highly unlikely that other mammals would have these same redundant pseudogenes in the same chromosomal locations, with the same mutations that cripple their normal functions."

http://www.talkorigins.org/faqs/comdesc/section4.html

As seen here, the TalkOrigins argument for evolution depends ENTIRELY on the belief that the insertions are random. If the insertions are not always random (which research is increasingly finding), the argument falls apart.

"There are similarities that cannot rationally be attributed to design. For example, an endogenous retroviral element (ERV) is a retrovirus (a parasite) that has become part of the genome. There are several kinds of ERVs, and they can insert themselves at random locations. Humans and chimps have thousands of such ERVs in common -- the same type of ERV at the same location in the genome (D. M. Taylor 2003)."

http://www.talkorigins.org/indexcc/CI/CI141.html

--Jzyehoshua 13:56, 21 November 2014 (EST)

As for the following source you provided, I think it actually harms your argument for ERVs. If as your source claims, "Retroviruses occasionally cross to other species, often distantly related ones, such as from gibbons to koalas", then that actually defeats the entire argument for a common ancestor. The entire argument for a common ancestor proven from ERVs relies on showing that the only way two species can have a similar ERV sequence is through common descent. If ERVs can simply cross freely between entirely different types of species, then I think you've sabotaged your own case for a common ancestor.

http://tinyurl.com/mmy9mvf

--Jzyehoshua 14:03, 21 November 2014 (EST)

As for Creationists inventing a cure for AIDS, maybe there are Creationist organizations out there with the resources to look for such a cure, I don't know. However, as I pointed out in the Public Policy section, the Creationist movement is not backed with billions of taxpayer dollars like the Evolutionist movement is, and resources are few and far between. Perhaps an institution like AiG or ICR might have the resources to pursue such a cure. However Creationism generally does not have the resources available to those who believe in Evolution, and finding Creationists with the means to perform such experimentation may prove difficult. If I had the resources to search for such a cure I would do so myself. At any rate, saying that Creationists should find a cure if they know the solution overlooks the lack of resources available to them.

http://creationwiki.org/Creationism2#Public_Policy

--Jzyehoshua 14:09, 21 November 2014 (EST)

It is ineffectual to argue semantics and ignore the facts. Surveys of retroviral integration sites typically show no duplication of locus within 500 samples. (Links already given). This means that the probability of independent coincidental integration to the same locus is, at most, 1/500. The probability of two such coincidences is 1/500 ^ 2. The probability of 200,000 coincidental integrations (the number of commonly located ERVs and ERV remnants in chimps and humans) is 1/500 ^200,000.

Non-orthologous (non commonly located) similar ERVs are irrelevant. All they show is that retroviruses can endogenize independently in different species. So what? It is missing the point to claim that this defeats the proof of common ancestry from commonly located ERVs.

Creationist organizations have not even tried to propose a methodology for developing a cure for AIDS. I consider it to be grossly irresponsible to try and sow doubts about the value of real science.Barry Desborough 23:53, 21 November 2014 (EST)

The surveys in question as seen from your first link earlier are "HIV integration site selection: Analysis by massively parallel pyrosequencing reveals association with epigenetic modifications" and "Retroviral DNA Integration: ASLV, HIV, and MLV Show Distinct Target Site Preferences." According to the first study:

"However, integration site selection in vivo is not random. HIV favors integration within active transcription units (Schroder et al. 2002; Wu et al. 2003; Mitchell et al. 2004; Barr et al. 2005, 2006; Ciuffi et al. 2005, 2006b; Lewinski et al. 2005, 2006)... PSIP1/LEDGF/p75-responsive genes were identified by transcriptional profiling and found to be favored integration targets for both HIV (Ciuffi et al. 2005; Berry et al. 2006) and another lentivirus, feline immunodeficiency virus (Kang et al. 2006). However, in cells depleted for PSIP1/LEDGF/p75, HIV integration was still favored in transcription units. Thus additional factors may be involved in guiding HIV integration (Ciuffi et al. 2005)."

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933515

Now from what I'm seeing of the paper, it sounds like there is more specificity in HIV integration, a key retrovirus, then had been predicted. Specific genes are being targeted, rather than the randomness claimed to prove a common ancestor.

Furthermore, specific ERVs are useful for specific genera. One ERV is ideally suited for sheep and they cannot reproduce without it. This would suggest that rather than just the result of a "past parasitic viral infection" as TalkOrigins claims, they may carry specific roles necessary to certain types of life.

http://www.sciencedaily.com/releases/2006/09/060911233630.htm

Is there a single specific ERV sequence you would point to to claim common ancestry? Just saying they all support common ancestry would be false as I can point to specific ERVs that show greater similarity between humans and other types of life then apes.

Again, I ran a BLAST of the V9H1F4 ERV and found the highest similarity scores were for the Carolina Anole, the Aardvark, and the Pigeon. Those are not what Evolutionists would term closely related. I ran several more ERV BLAST searches today and am seeing a number of human ERVs where there is more similarity to mice viruses than ape viruses. There is even similarity to sheep viruses (ovine enzootic). Here is one example, run on ERVK-19 (BLAST link will only work for a day or so and then the search would need to be re-run on the FASTA sequence). At any rate, there is similarity to other types of life then just chimps and apes.

http://blast.ncbi.nlm.nih.gov/Blast.cgi

http://www.uniprot.org/uniprot/Q9WJR5

--Jzyehoshua 13:05, 22 November 2014 (EST)

It is not similarity, but similarity plus PRECISELY CORRESPONDING LOCI that prove common ancestry. If you have any evidence of retroviruses repeatedly targetting precise loci, let's hear it. Otherwise your case is lost. (In fact, never got started.) Barry Desborough 13:11, 22 November 2014 (EST)

Again, I'm not convinced the loci are as specific as you think, which is why I asked for a specific ERV you would point to as proof of a common ancestor. Some of the ERV sequences I looked at show 90+% identicality to the human ERV for all types of life, not just apes. Even when there is a strong ape similarity to a given human ERV it's only around 93-95%, not 100% identicality. That's why I'd like to get into specific examples you think show a common ancestor, rather than this "all ERVs show a common ancestor" argument. --Jzyehoshua 13:29, 22 November 2014 (EST)

As for a methodology for curing AIDS, I would think the best way to approach it would be to start running BLAST searches on the largest HIV sequences possible. For example, these are HIV sequences sorted by length.

http://www.uniprot.org/uniprot/?query=hiv+AND+organism%3A"human+immunodeficiency+virus"&sort=length

I notice HIV seems to be a compilation of all these little chunks of code, so that one must examine each individually rather than the entire code at once (which I find highly inconvenient). At any rate, one would then want to begin a spreadsheet tracking the results from each sequence to get an overall idea of where the greatest similarity lies.

I would also recommend examining the specific transmission process when HIV is transferring to humans, rather than just the code itself. Figure out what the transmission trigger is and what organisms are most similar to HIV, to get an idea for potential cures. Then go from there to see how to affect HIV in different ways. --Jzyehoshua 13:19, 22 November 2014 (EST)

Answer me about locus specificity. You seem very confused about the issue of locus specificity. It is not just about ERV similarity, but about ERV similarity IN CORRESPONDING LOCATIONS. You want a specific ERV? Take your pick from any of the 200,000-odd locus-specific inherited retroviral integrations. Explain to me WITH EVIDENCE how it can have come to be where it is by coincidence, or design, with a probability of more than 1/500. http://www.evolutionarymodel.com/ervs.htm#Target_site_preference Barry Desborough 13:24, 22 November 2014 (EST)

Well, I already gave two different specific examples of ERVs that fail to support a common ancestor, the V9H1F4 and ERV-K19 ERV sequences. Both of them show stronger similarity to humans than apes. I suppose I can find a third example though. However, you still have yet to identify one specific ERV you would point to in support of a common ancestor. I notice the BLAST link on the ERV-K19 got posted incorrectly, this should be the BLAST result (which again will only work for a few hours).

http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=72FZC8KV014

--Jzyehoshua 21:09, 22 November 2014 (EST)

Here is a third example that shows more similarity between mice and humans than apes, ERVK-25.

http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=72GMTCA4014

http://www.uniprot.org/uniprot/P63136

Like I said, there are a number of ERVs which show more similarity to other types of life than apes.

--Jzyehoshua 21:28, 22 November 2014 (EST)

You continue to fail to address the issue of location, and thereby you continue to miss the entire point. A retrovirus can become endogenized independently in two different species, or it can become endogenized once in a common ancestor of two different species. In the first case, the ERVs will not appear in the same location in both species. This is not evidence that they never had a common ancestor, just that the retrovirus involved did not become endogenized in a common ancestor. In the second case, because the loci are common, it is highly probable that it is not by coincidence. It is more likely that both species have inherited the same ERV from a common ancestor. The more such common loci occur, the more certain it is that they originally endogenized in common ancestors. You ask for specific examples of orthologous ERVs. See Table 1 here, http://www.genetics.org/content/171/3/1183.full.pdf+html . But again, the answer to, "How many ERVs are shared, in common locations, between chimps humans?" is, "Virtually all of them." See http://www.evolutionarymodel.com/ervs.htm#Amount_of_Shared_ERVs . Unless you can show that retroviruses target specific DNA loci, inheritance from common ancestors remains the only explanation for commonly located ERVs. In fact we know (we do not just assume) that retroviruses do not target specific loci. Ignoring key facts is no answer to the case for common ancestry from commonly located ERVs. Barry Desborough 22:03, 22 November 2014 (EST)

Well, actually the ERVs I mentioned did involve specific loci. If I understand the math right, then if there's 92% query coverage for a mouse mammary tumor with a length of 954 and identicality of 48%, then it means that over a section of 92% of the code (or total of 878 loci) that 48% are identical to their human counterparts, or 421. Anyway, there are going to be thousands and thousands of loci similar between humans and mice or other types of life also when it comes to ERVs. Again, there are specific ERVs where there is stronger genetic similarity between humans and non-apes than apes like those I mentioned.

Even in cases like this ERV where you see high scores for pongo abelii (the orangutan) and saimiri boliviensis boliviensis (the squirrel monkey) you also see high scores for non-apes like heterocephalus glaber (the naked mole rat), oryctolagus cuniculus (the european rabbit), tupaia chinensis (the tree shrew), ictidomys tridecemlineatus (the chipmunk), and rattus norvegicus (the norwegian rat). There are even 790 scores there for felis catus (the housecat) and sus scrofa (the common pig) with 98% identicality to their human counterparts.

http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=742E96NT01R

http://www.uniprot.org/uniprot/Q9Y282

My point is that there are thousands of loci similar to other types of life when it comes to human ERVs, not just apes. I could find thousands of loci similar to their human counterparts from pigs and cats if I wanted to. I really think there is cherrypicking to make it appear there's a stronger case for ape-human descent here. Yes, there are some ERVs where there is a stronger link to apes, but as I've been pointing out there are other ERVs where there's a stronger link to other types of life than apes. However, the latter isn't convenient for the case for evolution, so it goes unmentioned except by creationists. --Jzyehoshua 11:38, 23 November 2014 (EST)

The evidence in other words only looks indisputable if comparing only between humans and apes genetically, not other types of life. You'll notice in these types of genetic arguments for evolution the only levels of similarity mentioned are between apes and humans, there is no mention of what the similarity is between humans and mice, cats, dogs, or anything else which would provide a frame of reference. --Jzyehoshua 11:55, 23 November 2014 (EST)

You are still confusing sequence similarity and locus correspondence! Give me one example of locus, not sequence, coincidence in species that evolutionary science says are distantly related. Barry Desborough 12:54, 23 November 2014 (EST)

Zoonoses

Something else I would point out is that ERVs appear to be a form of zoonoses. They appear to spread the same way, through animal contact.

http://en.wikipedia.org/wiki/Zoonosis

They are cured in the same way, through vaccines. In fact, rabies vaccine even acts as something of a curative for HIV. Rabies though is more closely linked to bats than apes.

http://www.sciencedaily.com/releases/2007/04/070403153910.htm

--Jzyehoshua 21:22, 22 November 2014 (EST)

Do you mean ERVs or retroviruses? Barry Desborough 22:02, 22 November 2014 (EST)

Referring to ERVs which are of course retroviruses. --Jzyehoshua 11:38, 23 November 2014 (EST)

ERVs are the inherited remnants of retroviral integrations (proviruses, in the jargon). They are not virions (viable exogenous retroviruses). As such, exogenous retroviruses are irrelevant to the proof of common ancestry that is provided by correspondingly located ERVs. Barry Desborough 12:59, 23 November 2014 (EST)

The Creationist Explanation for Apparently Orthologous ERVs

Given that their promoters are in the appropriate relative position with respect to the genes they regulate, the position of the regulator-gene ensemble in the entire DNA is functionally insignificant. They will work the same way wherever they are located. Given this, given that the function of reverse transcriptase is to "read" RNA and generate a DNA version, given that integrase functions to splice reverse-transcribe DNA into nuclear DNA, and given that long terminal repeats (LTRs) are so constructed as to make polymerase transcribe them, despite the fact that they are promoters and not protein-coding genes, how does the creationist "paradigm" explain the presence of so many of these structures in exactly corresponding locations in what evolutionary science has already concluded are closely related species? Yes, certain sub-components of some ERVs perform functions useful, even sometimes vital, to their owners, but these could have been "designed" without apparent orthology, without reverse transcriptase, without integrase and without transcribable LTRs. Why weren't they? Barry Desborough 23:20, 24 November 2014 (EST)